9FXZ | pdb_00009fxz

Galectin-8 N-terminal carbohydrate recognition domain in complex with 4-(bromophenyl)phthalazinone D-galactal ligand

• PDB DOI: https://doi.org/10.2210/pdb9FXZ/pdb
• Entry: 9FXZ supersedes: 8CM8

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-02 Released: 2025-07-16 
• Deposition Author(s): Van Klaveren, S., Hakansson, M., Diehl, C., Nilsson, N.J.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.157 (DCC) 

Starting Model: experimental

Literature

Galectin-8N-Selective 4-Halophenylphthalazinone-Galactals Double pi-Stack in a Unique Pocket.

van Klaveren, S., Hassan, M., Hakansson, M., Johnsson, R.E., Larsson, J., Jakopin, Z., Anderluh, M., Leffler, H., Tomasic, T., Nilsson, U.J.

(2024) ACS Med Chem Lett 15: 1319-1324

• PubMed: 39140038 
• DOI: https://doi.org/10.1021/acsmedchemlett.4c00212
• Primary Citation Related Structures: 
  9FXZ


• PubMed Abstract: 
  

  Galectin-8 contains two different carbohydrate recognition domains (CRDs). Selective inhibitors for at least one CRD are desirable for galectin-8 biology studies and potentially for pharmacological purposes. Structure-guided design led to the discovery of potent and selective glycomimetic-heterocycle hybrid ligands, with a 4-( p -bromophenyl)phthalazinone derivative displaying a 34 μM K _d for galectin-8N (N-terminal CRD), no binding to galectin-8C (C-terminal CRD), -1, -3, -4N, -7, -9C, or -9N, and >40-fold selectivity over galectin-4C. Selectivity was achieved with the halogenated 4-phenylphthalazinone moiety occupying a galectin-8N-specific sub-pocket. A 1.30 Å resolution X-ray structure revealed the phthalazinone moiety stacking with Arg45 and the 4-bromophenyl moiety stacking both Arg59 and Tyr141 of galectin-8N. Physicochemical and in vitro ADME studies revealed a desirable LogD, which also translated to good passive permeability. The chemical, microsome, and plasma stability support these compounds as promising tool compounds and candidates for hit-to-lead optimization.

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Organizational Affiliation: 
• Department of Chemistry, Faculty of Science, Lund University, Naturvetarvägen 14, 223 62, Lund, Sweden.
Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden.
Red Glead Discovery AB, Medicon Village, SE-223 81, Lund, Sweden.
Department of Laboratory Medicine, Section MIG, Lund University, BMC-C1228b, Klinikgatan 28, 221 84, Lund, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.66 kDa 
• Atom Count: 2,803 
• Modeled Residue Count: 296 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-8	A, B	317	Homo sapiens	Mutation(s): 0  Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens) Explore O00214  Go to UniProtKB:  O00214
PHAROS:  O00214 GTEx:  ENSG00000116977

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V19 (Subject of Investigation/LOI)	C [auth A], E [auth B]	4-(4-bromophenyl)-2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]phthalazin-1-one C21 H19 Br N2 O5 NMCPEIVYVRUQEU-QWFCFKBJSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.157 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.71	α = 90
b = 62.28	β = 90
c = 84.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Van Klaveren, S., Hakansson, M., Diehl, C., Nilsson, N.J.
• This entry supersedes: 8CM8

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	765581

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release